Contacts of the strand formed by residues 562 - 569 (chain A) in PDB entry 2WMH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 562 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536A PHE* 3.8 3.8 - - - -
555A ILE* 4.1 26.7 + - + +
556A SER* 3.4 19.1 - - - -
557A GLY* 3.6 32.3 + - - -
558A ASP 3.5 16.4 - - - -
559A LYS* 5.4 1.6 - - - -
560A ASN* 3.7 4.6 - - - -
561A HIS* 1.3 81.7 + - - +
563A THR* 1.3 73.5 + - - +
564A TYR* 4.1 19.7 - + - -
579A VAL* 4.6 1.6 - - + -
580A ASN 3.1 13.2 - - - +
581A HIS* 3.7 0.7 - - + -
585A VAL* 3.5 29.2 - - + -
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Residues in contact with THR 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536A PHE* 4.3 13.2 - - + -
562A TYR* 1.3 83.0 - - - +
564A TYR* 1.3 67.3 + - - +
579A VAL* 3.5 3.5 - - - +
580A ASN* 2.8 54.2 + - - +
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Residues in contact with TYR 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A ILE* 4.7 1.8 - - + +
555A ILE* 3.7 38.8 - - + +
562A TYR* 4.1 13.9 - + - -
563A THR* 1.3 83.4 + - - +
565A THR* 1.3 68.4 + - - +
566A GLU* 3.9 30.2 + - + -
577A ILE* 3.6 30.1 - - + -
578A THR 3.1 12.8 - - - +
579A VAL* 4.2 8.1 - - + -
580A ASN* 4.5 2.2 - - - -
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Residues in contact with THR 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A TYR* 1.3 79.9 - - - +
566A GLU* 1.3 64.5 + - - +
576A THR 3.9 0.2 - - - +
577A ILE* 3.4 5.7 - - - +
578A THR* 2.9 51.6 + - + +
580A ASN* 5.2 6.5 - - - +
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Residues in contact with GLU 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A PRO 4.7 4.9 - - - +
553A ILE* 3.8 16.3 + - - +
564A TYR* 3.9 28.8 + - + -
565A THR* 1.3 81.8 + - - +
567A ASN* 1.3 63.6 + - - +
575A TYR* 2.7 41.5 + - + +
576A THR 3.3 4.7 - - - -
577A ILE* 4.3 1.8 - - + -
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Residues in contact with ASN 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A GLU* 1.3 78.7 - - - +
568A TRP* 1.3 76.5 + - - +
569A ASP* 4.6 2.3 + - - +
574A VAL 3.7 1.2 - - - +
575A TYR* 3.3 8.4 - - - -
576A THR* 2.8 53.5 + - + +
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Residues in contact with TRP 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A HIS* 4.5 9.2 - - + -
549A HIS* 3.8 13.5 - - - -
550A LYS* 3.5 39.4 - - + +
551A PRO* 3.7 17.7 - - + -
567A ASN* 1.3 83.5 + - - +
569A ASP* 1.3 59.2 + - - +
570A GLU* 3.3 46.9 - - + +
573A HIS* 3.5 56.1 - + - -
574A VAL 3.5 15.3 - - - -
575A TYR* 3.6 23.8 - - + -
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Residues in contact with ASP 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567A ASN* 5.4 1.8 - - - +
568A TRP* 1.3 72.5 - - - +
570A GLU* 1.3 59.8 + - - +
571A ASN* 3.0 21.1 + - - +
572A THR* 3.2 30.4 + - - +
573A HIS* 2.7 36.9 + - - -
574A VAL* 2.9 16.6 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il